Zuma, whose presidency has been engulfed by multiple scandals, had fought to block the release of the Public Protector's report, until his lawyers made a surprise U-turn and dropped their legal appeal earlier in the day.
The report was released hours later, further undermining Zuma after a series of court rulings that have tarnished his time in office and fuelled calls for him to stand down.
The investigation probed accusations that Zuma allowed the Guptas, a wealthy Indian business family, to have undue influence over government, including letting them choose some cabinet ministers.
Van Rooyen, a little-known Zuma loyalist, was removed as finance minister just four days later following a market plunge, investor panic and waves of political outrage.
In the report, the Public Protector said it "brings to the notice of the National Prosecuting Authority... Those matters identified in this report where it appears crimes have been committed".
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